Analyze Linkage disequilibrium between SNPs in a Gene Region using Haploview 4.2

Question

[davidenoma]

I have a set of SNPs that are within a particular gene region.

I intend to use the Haploview 4.2. software to analyze the Linkage Disequilibrium between variants.

How might I create the input data file for a set of SNPs that I want to analyze with haploview?

Are there alternatives to analyze the Linkage disequilibrium between SNPs?

Answer 1

[abdin-marwa]

Hi, from my new experience with haploview I can tell you about how to create the input data file, firstly visit : https://www.broadinstitute.org/haploview/input-file-formats to know how to manually edit your files to the acceptable format. if your results are on excel you can convert them first to text using save as (Ms- Dos text) but write the extension .hmp first this gives you for example xxxxx.hmp.txt a text file which can be further converted into (.ped) and (.info) for data file and marker info file respectively. How? simply by renaming the files and removing the extension .txt and typing .ped or .info instead. now, these files are readable by haploview. I wish this would help

[davidenoma]

Hi, @abdin I have read through the documentation of the file formats required for haploview.

What I need are the specific column values that are required for any of the file format types required of haploview. Do you have any that you have used?

[abdin-marwa]

Hi, David, I am not sure about understanding your question. but I will refer you to a previous conversation that may help you Haploview formats